ibdsim2 2.0.0

Breaking changes

As of version 2.0.0, the main data structure for IBD segments includes both megabase (MB) and centiMorgan (CM) coordinates. This allows the user to choose length unit in all downstream analyses. However, the new format is not compatible with previous versions of the package.
ibdsim() has a new argument simplify1, by default TRUE. This means that ibdsim(..., N = 1) now simply returns a matrix, without the outer list layer. This typically the desired behaviour in interactive use, especially when piping. To enforce a list output, add simplify1 = FALSE.

All downstream functions depending on segment lengths (e.g. segmentStats() and plotSegmentDistribution()) have a new argument unit, allowing the user to choose between “cm” (centiMorgan) and “mb” (megabases).
haploDraw() has nicer default colours and automatically produces sensible margins.
New (experimental) function karyoHaploid() for visualising IBD segments in karyogram plots.
convertPos() has been rewritten using Rcpp, making it much more efficient.
General overhaul of documentation, examples and README.

Fix labelling bug in haploDraw().
profileSimIBD() has been overhauled, fixing several glitches and with significant speed improvements. Note: Simulations with a given seed may differ across versions.
The internal dataset decode19 has been recompiled, updating some attributes. This should not affect regular users.

New function segmentStats() for summarising the segments identified by findPattern().
findPattern() has a new argument cutoff for excluding short segments.
findPattern() can detect more patterns: the argument pattern now accepts entries autozygous and heterozygous.
findPattern() is much faster now, mostly due to a new implementation of the internal mergeSegments()
New function extractIds() replaces the previous (non-exported) extractIdsFromSegmentSummary().
Updated README, including links to Shiny app.

Fixed wrong length attribute of loadMap() when uniform = F and sexAverage = T.

ibdsim() now allows map to be a list of chromosome maps.
New function findPattern() for identifying IBD patterns in simulation outputs.
New function convertPos() for converting between genetic and physical positions.
New functions mapLen() and physRange() for retrieving map info.
profileSimIBD() now sorts the genotypes before returning.
README is updated and expanded.

The previous built-in recombination map (based on Kong et al., 2010) is replaced with one based on Halldorsson et al. (2019), using GRCh38 coordinates. For reasons of speed and efficiency, the built-in map is a thinned version of the published map, keeping around 60 000 data points.

New function haploDraw() for visualising IBD patterns
The internal data structure for genetic maps has been rewritten.
New functions loadMap() and customMap() for loading built-in and user-prepared maps.